Although I haven't got any of the Pro Series II kits yet, I have gotten some of the 29mm motor retainers - these are the same as are being used in the kits and they fit a standard 29mm motor tube. Plus, as was mentioned earlier, the new Pro Series II motors are simply relabeled Aerotech single use motors, and these can be used interchangeably with the 29mm RMS motors (at least diameter-wise). You'll probably want to run each rocket through Rocksim or Open Rocket to find out the optimal delays, and if you use an adapter, they should also fly well on 24mm reloads as well. The E9 motors may not be strong enough to lift it, but the new E12 motors that are coming might (I haven't looked at the thrust curves and don't know what the max lift weight will be for the E12, so I don't know for sure).
In short, yes, you will be able to use 29mm RMS motors in these kits.